deepSNV——一个用于亚克隆变异呼叫的R包。1.13.8更新中的更改* Shearwater ML (Inigo Marticorena) * Rhtslib支持(David Jones) 1.11.1版本中的更改错误修复*报告正确的汇总表(…、价值= " VCF ");感谢David Gacquer。1.7.4版本更改(2013-09-28)更新*仅使用狄利克雷先验进行控制*从1.99更改回版本号。X到1.7。版本1.99.3的变化(2013-07-25)更新* shearwater vignette的一些变化*重命名参数pi。基因和π。makePrior()中的backgr错误修复*修正了bf2Vcf()中没有变量被调用时的错误1.99.2版本的变化(2013-07-11)更新*更新了CITATION *在bam2R中添加了verbose选项以抑制输出*更改模式()为loadAllData()的值改为“整数”错误修复*修正了在bf2Vcf()中只调用一个变量时的错误1.99.1版本的变化(2013-06-25)更新*使用knitr进行更漂亮的小插曲*包括shearwater小插曲错误修复*修正了bf2Vcf()中删除的问题* makePrior()adds background on all sites Changes in version 1.99.0 (2013-04-30) Updates * New shearwater algorithm * Including VCF output through summary(deepSNV, value="VCF") Changes in version 1.3.3 (2012-09-14) Updates * Changed CITATION * Updated documentation * Updated biocViews * Using roxygen2 for generating man pages Changes in version 1.3.2 (2012-04-10) Updates * New devel version, identical to release 1.2.3 Changes in version 1.2.3 (2012-04-10) Bugfixes * Fixed Vignette * Jumped a few numbers due to automated bioc version numbering Changes in version 1.0.0 (2012-03-29) Updates * Added CITATION file * Made NEWS (this file) R-readable * Changed Vignette Changes in version 0.99.3 Bugfixes * Fixed error in summary() when there were no significant SNVs. * Some fixes if only a single column of the alignment is selected Changes in version 0.99.2 (2012-01-20) Updates * Changed plot to S3 method (to avoid warning in R-devel) Changes in version 0.99.1 (2012-01-06) Updates * Added small .bam example files test.bam, control.bam with 100 positions. * Modified man pages for bam2R() * Modified man page for coordinates() * Corrected example of consensusSequence() * Compressed .RData files with tools::resaveRdaFiles * Changed vignette to attach data, rather than load remotely. * Argument "regions" of deepSNV can be a GRanges object. Changes in version 0.99.0 (2011-12-21) Updates * Added BiocViews field * Added HIVmix data * Added new examples * Registered bam2R with R_registerRoutines * New accessor functions "test", "control", "p.val", and "coordinates" * Updated vignette Changes in version 0.9.5 Updates * "summary" now reports additional columns from regions slot. Bugfixes * drop=FALSE in subsetting and summary. Changes in version 0.9.4 Updates * Directly link to static samtools library provided by Rsamtools * Load example .bam files over http Changes in version 0.9.3 * Added beta-binomial model * Extended documentation * Use summary instead of significantSNV Changes in version 0.9.2 * Minor bugfixes Changes in version 0.9.1 Minor bugfixes Changes in version 0.9.0 Pre-release